How was the “amen”, being a Latin word and therefore “Catholic”, retained by virtually all denominations of Protestants?

Do you mean the word "amen"? It's not Latin, it's Hebrew, and it's used pretty frequently in the Bible.

In Hebrew אָמֵן means something like "truly" or "so be it." In Deuteronomy 27 it's a cry of assent: the Levites are supposed to state a law (e.g., "Cursed be anyone who misleads a blind person" NRSV) and the people are supposed to consent to that law by responding, "So be it!" By the Second Temple period it appears in prayers and liturgical practice. For example, in Tobit 8 (2nd or 3rd century BCE) it's used at the end of a prayer. Modern Jews use it prayers like the Kaddish.

It's very frequent in the Gospels, especially John, in constructions like ἀμὴν ἀμὴν λέγω ὑμῖν (Truly, truly I say to you...), usually the punchline in some teaching of Jesus. Examples: John 5:24; 10:7. It shows up in places like Romans 1:25, where it indicates that Paul is quoting a liturgical formula. In some manuscripts it's also the very last word of Revelation, and a lot of English translations therefore retain it as the last word of the Christian Bible (the latest Nestle-Aland edition has it as a variant reading, but it has strong and major manuscripts witnessing to it).

So, to answer your question, Protestants retained it because it's an indelible part of the Christian liturgical tradition, inherited from the Jewish liturgical tradition.